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Figure 2
Comprehension of N-linked glycosylation trees that has been built into Coot. For ease of use, the trees are partitioned into five major types (four of which are shown). The user decides which tree type is to be built, and only the given linked residue types are then available for any position in the tree. The rationale for these categories is the biochemical distinction of the major types of glycan structures that could arise from the common expression systems used to generate structures deposited in the PDB. In addition, some finer distinctions are made (for example, between plant and mammalian variants of complex and hybrid-type glycans) to help the user avoid or accommodate species-specific differences. In the case of plants, these include the specific α1–3-fucose off the asparagine-linked NAG and β-xylose linked to the β-D-mannose (BMA) (Schoberer & Strasser, 2017BB53). The aim is to help to reduce errors when users are less familiar with the residues and linkages that should be expected for particular types of glycan (Crispin et al., 2007BB18). The top row represents the full tree that is available for a given tree mode. [Unfortunately, at the present time, the addition of sialic acid to the galactose in the `Biantennary (Mammal)' and `Hybrid (Mammal)' trees is not available owing to unresolved compatibility problems with the dictionary linking information.] Using the LMA mode, Coot has been used to build representative examples for each tree type. The second row shows the cartoon for the built tree using the nomenclature of the Consortium for Functional Glycomics (CFG) with link sensitivity. The third row shows the electron density represented by the cartoon above. The carbon atoms of the individual monosaccharides are coloured using the CFG convention.

Journal logoSTRUCTURAL
ISSN: 2059-7983
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